No it will not. Becuase details appearing in 26AS is based on quarterly filing of TDS return wherein there is no column for section 10 deductions/exemptions viz HRA, conveyance allowance. Therefore, they must need to show salary gross and not net. However, in Q4 TDS return there are two seperate annexures Annexure I which is normal TDS deduction details based on gross salary and Annexure II is having computation for each employee, their section 10 exemptions, loss under house property (interest on housing loan) their Chapter VI-A deductions, other income reported,etc. Details appearing in Annexure -II of your employer TDS return not available for verification to deductee as the same can only been visible at the Income Tax department end. your FOrm 16 devided into two parts. Part A is nothing but reflection of your 26AS data in form of certificate. However Part B is entire computation of how your taxable income arrived at.
Employer (TDS deductor) always ensures that your Form 16 Part B should always tallied with what they have mentioned in Annexure II to avoid future problems. In case demand comes, just show your Form 16 both parts to AO duly authenticated by your employer.
Thanks and Regards,
Manoj B. Gavali